PartitionFinder: Difference between revisions

Revision as of 14:28, 17 October 2012

Description

PartitionFinder and PartitionFinderProtein are free open source programs for selecting best-fit partitioning schemes and models of molecular evolution for nucleotide and amino acid alignments. They take the hard work out of comparing partitioning schemes, and are useful in any situation where you wish to compare or select partitioning schemes or models of molecular evolution. Both programs come together as a single download. Click below to get the appropriate download for your system.

Required Modules

modules documentation

Serial

partitionfinder

System Variables

HPC_{{#uppercase:partitionfinder}}_DIR - installation directory

How To Run

Run PartitionFinder programs for nt or aa model analysis respectively as

PartitionFinder.py -p X DIRECTORY

and

PartitionFinderProtein.py -p X DIRECTORY

once the partitionfinder module is loaded where "X" is the number of compute cores requested in the job script.

Citation

If you publish research that uses partitionfinder you have to cite it as follows: Please cite Lanfear et al. (2012) if you use the tool for published research.

@@ Line 34: / Line 34: @@
 {{#if: {{#var: exe}}|==How To Run==
-PartitionFinder is a python application, so the direct way to run it is to use <code>python $HPC_PARTITIONFINDER_DIR/PartitionFinder.py -p X DIRECTORY</code> or <code>python $HPC_PARTITIONFINDER_DIR/PartitionFinderProtein.py -p X DIRECTORY</code> for nt or aa models respectively once the <code>partitionfinder</code> module is loaded where "X" is the number of compute cores requested in the job script, ... are any addition options and DIRECTORY is the directory with the configuration and input files. However, we have a convenience scripts that allow you to run PartitionFinder directly for either nt or aa analysis as <code>partitionfindernt -p X NUCLEOTIDE_DIRECTORY</code> or <code>partitionfinderaa -p X AMINOACID_DIRECTORY</code> once the <code>partitionfinder</code> module is loaded.
+Run PartitionFinder programs for nt or aa model analysis respectively as
+ PartitionFinder.py -p X DIRECTORY
+and
+ PartitionFinderProtein.py -p X DIRECTORY
+once the <code>partitionfinder</code> module is loaded where "X" is the number of compute cores requested in the job script.
 |}}
 <!--Configuration-->